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From: izmiyati razikin [mailto:izmiyati@novaglobal.com.sg]
Sent: Monday, 25 June, 2012 11:01 PM
To: 'galaxy-dev@lists.bx.psu.edu'
Subject: unable to start galaxy

Hello,

I’m having problem starting up galaxy. I’m using RHEL 5.3 which comes with python 2.4.3. So I compiled python 2.6.5. I’ve created a symbolic link and set it in PATH. Yet I’m unable to start galaxy.

Thanks in advance for help!

Fetch successful.

Starting subprocess with file monitor

Traceback (most recent call last):

  File "./scripts/paster.py", line 34, in <module>

    command.run()

  File "/home/software/apps/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 84, in run

    invoke(command, command_name, options, args[1:])

  File "/home/software/apps/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 123, in invoke

    exit_code = runner.run(args)

  File "/home/software/apps/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 218, in run

    result = self.command()

  File "/home/software/apps/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 276, in command

    relative_to=base, global_conf=vars)

  File "/home/software/apps/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 313, in loadapp

    **kw)

  File "/home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 204, in loadapp

    return loadobj(APP, uri, name=name, **kw)

  File "/home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 224, in loadobj

    global_conf=global_conf)

  File "/home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 248, in loadcontext

    global_conf=global_conf)

  File "/home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 278, in _loadconfig

    return loader.get_context(object_type, name, global_conf)

  File "/home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 413, in get_context

    section)

  File "/home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 458, in _context_from_explicit

    value = import_string(found_expr)

  File "/home/software/apps/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 18, in import_string

    return pkg_resources.EntryPoint.parse("x="+s).load(False)

  File "/home/software/apps/galaxy-dist/lib/pkg_resources.py", line 1954, in load

    entry = __import__(self.module_name, globals(),globals(), ['__name__'])

  File "/home/software/apps/galaxy-dist/lib/galaxy/web/buildapp.py", line 19, in <module>

    from galaxy import config, jobs, util, tools

  File "/home/software/apps/galaxy-dist/lib/galaxy/jobs/__init__.py", line 4, in <module>

    from galaxy import util, model

  File "/home/software/apps/galaxy-dist/lib/galaxy/model/__init__.py", line 13, in <module>

    import galaxy.datatypes.registry

  File "/home/software/apps/galaxy-dist/lib/galaxy/datatypes/registry.py", line 6, in <module>

    import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex, wsf

  File "/home/software/apps/galaxy-dist/lib/galaxy/datatypes/tabular.py", line 15, in <module>

    from sniff import *

  File "/home/software/apps/galaxy-dist/lib/galaxy/datatypes/sniff.py", line 8, in <module>

    from galaxy.datatypes.binary import unsniffable_binary_formats

  File "/home/software/apps/galaxy-dist/lib/galaxy/datatypes/binary.py", line 12, in <module>

    from bx.seq.twobit import TWOBIT_MAGIC_NUMBER, TWOBIT_MAGIC_NUMBER_SWAP, TWOBIT_MAGIC_SIZE

  File "/home/software/apps/galaxy-dist/eggs/bx_python-0.7.0_494c2d1d68b3_rebuild1-py2.6-linux-x86_64-ucs2.egg/bx/seq/__init__.py", line 7, in <module>

    from bx.seq.core import *

  File "/home/software/apps/galaxy-dist/eggs/bx_python-0.7.0_494c2d1d68b3_rebuild1-py2.6-linux-x86_64-ucs2.egg/bx/seq/core.py", line 10, in <module>

    import fasta, nib, qdna

  File "/home/software/apps/galaxy-dist/eggs/bx_python-0.7.0_494c2d1d68b3_rebuild1-py2.6-linux-x86_64-ucs2.egg/bx/seq/nib.py", line 28, in <module>

    import _nib

ImportError: /home/software/apps/galaxy-dist/eggs/bx_python-0.7.0_494c2d1d68b3_rebuild1-py2.6-linux-x86_64-ucs2.egg/bx/seq/_nib.so: undefined symbol: Py_InitModule4_64

[240223 refs]

[55760 refs]

Rgds,

Izy